As your history says, there was history of some accident with the uncle of the girl, which might have caused deformed torso and then short stature.
The children's of that man are absolutely normal, so I don't think it might be due to some genetic defects. As genes for height are not single genes, there are multiple locus of height controlling genes in various chromosomes.
"There are about 50 genes and regions of the genome have been associated with height to date."(source:http://www.ncbi.nlm.nih.gov/pubmed/19818695)
So there is no need to worry, as your son's progeny will be absolutely fine in regard to height as far as genetic diseases are concerned.(excluding environmental and nutritional causes of dwarfism
hope my info helped you
Dr Hari Om Chandrakar